Starting phenix.real_space_refine on Sat Aug 8 18:56:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdp_17617/08_2026/8pdp_17617.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 130 5.16 5 C 18820 2.51 5 N 5190 2.21 5 O 5950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30160 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Restraints were copied for chains: C, G, J, M, P, S, V, Y, 1, D, H, K, N, Q, T, W, Z, 2, F, I, L, O, R, U, X, 0, 3 Time building chain proxies: 3.18, per 1000 atoms: 0.11 Number of scatterers: 30160 At special positions: 0 Unit cell: (192.15, 192.15, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 70 15.00 O 5950 8.00 N 5190 7.00 C 18820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6880 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 20 sheets defined 69.2% alpha, 5.1% beta 0 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN B 13 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 14' Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.528A pdb=" N GLN D 13 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 14 " --> pdb=" O ILE D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 10 through 14' Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN H 13 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU H 14 " --> pdb=" O ILE H 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 10 through 14' Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN J 150 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 251 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 301 through 306 Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 361 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN K 13 " --> pdb=" O ASP K 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 14 " --> pdb=" O ILE K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 14' Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN M 150 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 275 through 280 Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 301 through 306 Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN N 13 " --> pdb=" O ASP N 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU N 14 " --> pdb=" O ILE N 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 10 through 14' Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG P 189 " --> pdb=" O ARG P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 198 Processing helix chain 'P' and resid 202 through 217 Processing helix chain 'P' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER P 222 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 251 Processing helix chain 'P' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG P 260 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 274 Processing helix chain 'P' and resid 275 through 280 Processing helix chain 'P' and resid 281 through 296 Processing helix chain 'P' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY P 300 " --> pdb=" O PRO P 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 297 through 300' Processing helix chain 'P' and resid 301 through 306 Processing helix chain 'P' and resid 318 through 332 Processing helix chain 'P' and resid 344 through 361 Processing helix chain 'Q' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN Q 13 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 10 through 14' Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU S 47 " --> pdb=" O GLU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN S 150 " --> pdb=" O PRO S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 171 removed outlier: 3.825A pdb=" N LYS S 171 " --> pdb=" O LEU S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG S 189 " --> pdb=" O ARG S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 251 Processing helix chain 'S' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 Processing helix chain 'S' and resid 275 through 280 Processing helix chain 'S' and resid 281 through 296 Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'T' and resid 10 through 14 removed outlier: 3.528A pdb=" N GLN T 13 " --> pdb=" O ASP T 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU T 14 " --> pdb=" O ILE T 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 10 through 14' Processing helix chain 'V' and resid 9 through 20 Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'V' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 75 through 86 Processing helix chain 'V' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN V 150 " --> pdb=" O PRO V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG V 189 " --> pdb=" O ARG V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 198 Processing helix chain 'V' and resid 202 through 217 Processing helix chain 'V' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER V 222 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 251 Processing helix chain 'V' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG V 260 " --> pdb=" O GLN V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 274 Processing helix chain 'V' and resid 275 through 280 Processing helix chain 'V' and resid 281 through 296 Processing helix chain 'V' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY V 300 " --> pdb=" O PRO V 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 297 through 300' Processing helix chain 'V' and resid 301 through 306 Processing helix chain 'V' and resid 318 through 332 Processing helix chain 'V' and resid 344 through 361 Processing helix chain 'W' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN W 13 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU W 14 " --> pdb=" O ILE W 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 10 through 14' Processing helix chain 'Y' and resid 9 through 20 Processing helix chain 'Y' and resid 37 through 39 No H-bonds generated for 'chain 'Y' and resid 37 through 39' Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU Y 47 " --> pdb=" O GLU Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 75 Processing helix chain 'Y' and resid 75 through 86 Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.629A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.616A pdb=" N GLN Y 150 " --> pdb=" O PRO Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 190 removed outlier: 3.922A pdb=" N ARG Y 189 " --> pdb=" O ARG Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 Processing helix chain 'Y' and resid 202 through 217 Processing helix chain 'Y' and resid 218 through 233 removed outlier: 3.715A pdb=" N SER Y 222 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 251 Processing helix chain 'Y' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG Y 260 " --> pdb=" O GLN Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 274 Processing helix chain 'Y' and resid 275 through 280 Processing helix chain 'Y' and resid 281 through 296 Processing helix chain 'Y' and resid 297 through 300 removed outlier: 3.522A pdb=" N GLY Y 300 " --> pdb=" O PRO Y 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 297 through 300' Processing helix chain 'Y' and resid 301 through 306 Processing helix chain 'Y' and resid 318 through 332 Processing helix chain 'Y' and resid 344 through 361 Processing helix chain 'Z' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN Z 13 " --> pdb=" O ASP Z 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU Z 14 " --> pdb=" O ILE Z 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 10 through 14' Processing helix chain '1' and resid 9 through 20 Processing helix chain '1' and resid 37 through 39 No H-bonds generated for 'chain '1' and resid 37 through 39' Processing helix chain '1' and resid 40 through 51 removed outlier: 3.844A pdb=" N LEU 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 75 Processing helix chain '1' and resid 75 through 86 Processing helix chain '1' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 151 removed outlier: 3.615A pdb=" N GLN 1 150 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 171 removed outlier: 3.824A pdb=" N LYS 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 175 through 190 removed outlier: 3.921A pdb=" N ARG 1 189 " --> pdb=" O ARG 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 198 Processing helix chain '1' and resid 202 through 217 Processing helix chain '1' and resid 218 through 233 removed outlier: 3.716A pdb=" N SER 1 222 " --> pdb=" O VAL 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 251 Processing helix chain '1' and resid 256 through 268 removed outlier: 3.658A pdb=" N ARG 1 260 " --> pdb=" O GLN 1 256 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 274 Processing helix chain '1' and resid 275 through 280 Processing helix chain '1' and resid 281 through 296 Processing helix chain '1' and resid 297 through 300 removed outlier: 3.521A pdb=" N GLY 1 300 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 297 through 300' Processing helix chain '1' and resid 301 through 306 Processing helix chain '1' and resid 318 through 332 Processing helix chain '1' and resid 344 through 361 Processing helix chain '2' and resid 10 through 14 removed outlier: 3.527A pdb=" N GLN 2 13 " --> pdb=" O ASP 2 10 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU 2 14 " --> pdb=" O ILE 2 11 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 10 through 14' Processing sheet with id=1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.188A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU G 111 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'J' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'J' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU J 111 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'M' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'M' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU M 111 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'P' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR P 33 " --> pdb=" O VAL P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'P' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU P 111 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'S' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU S 111 " --> pdb=" O LEU S 100 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'V' and resid 32 through 35 removed outlier: 6.188A pdb=" N THR V 33 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'V' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU V 111 " --> pdb=" O LEU V 100 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR Y 33 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'Y' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU Y 111 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain '1' and resid 32 through 35 removed outlier: 6.189A pdb=" N THR 1 33 " --> pdb=" O VAL 1 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain '1' and resid 96 through 104 removed outlier: 7.620A pdb=" N LEU 1 111 " --> pdb=" O LEU 1 100 " (cutoff:3.500A) 1680 hydrogen bonds defined for protein. 4920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9700 1.34 - 1.46: 5244 1.46 - 1.57: 15416 1.57 - 1.69: 130 1.69 - 1.81: 230 Bond restraints: 30720 Sorted by residual: bond pdb=" C ALA M 310 " pdb=" N GLY M 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA 1 310 " pdb=" N GLY 1 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA G 310 " pdb=" N GLY G 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA V 310 " pdb=" N GLY V 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.06e+00 bond pdb=" C ALA S 310 " pdb=" N GLY S 311 " ideal model delta sigma weight residual 1.335 1.325 0.010 9.80e-03 1.04e+04 1.04e+00 ... (remaining 30715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39431 1.20 - 2.39: 1845 2.39 - 3.59: 348 3.59 - 4.79: 56 4.79 - 5.98: 30 Bond angle restraints: 41710 Sorted by residual: angle pdb=" N LYS V 55 " pdb=" CA LYS V 55 " pdb=" CB LYS V 55 " ideal model delta sigma weight residual 109.87 113.28 -3.41 1.63e+00 3.76e-01 4.38e+00 angle pdb=" N LYS G 55 " pdb=" CA LYS G 55 " pdb=" CB LYS G 55 " ideal model delta sigma weight residual 109.87 113.28 -3.41 1.63e+00 3.76e-01 4.38e+00 angle pdb=" N LYS Y 55 " pdb=" CA LYS Y 55 " pdb=" CB LYS Y 55 " ideal model delta sigma weight residual 109.87 113.27 -3.40 1.63e+00 3.76e-01 4.34e+00 angle pdb=" N LYS J 55 " pdb=" CA LYS J 55 " pdb=" CB LYS J 55 " ideal model delta sigma weight residual 109.87 113.27 -3.40 1.63e+00 3.76e-01 4.34e+00 angle pdb=" N LYS S 55 " pdb=" CA LYS S 55 " pdb=" CB LYS S 55 " ideal model delta sigma weight residual 109.87 113.25 -3.38 1.63e+00 3.76e-01 4.30e+00 ... (remaining 41705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 16899 16.59 - 33.19: 1451 33.19 - 49.78: 330 49.78 - 66.37: 150 66.37 - 82.96: 130 Dihedral angle restraints: 18960 sinusoidal: 8250 harmonic: 10710 Sorted by residual: dihedral pdb=" C4' C 3 74 " pdb=" C3' C 3 74 " pdb=" C2' C 3 74 " pdb=" C1' C 3 74 " ideal model delta sinusoidal sigma weight residual 36.34 -34.32 70.67 1 3.10e+00 1.04e-01 6.68e+02 dihedral pdb=" C4' C F 74 " pdb=" C3' C F 74 " pdb=" C2' C F 74 " pdb=" C1' C F 74 " ideal model delta sinusoidal sigma weight residual 36.34 -34.32 70.66 1 3.10e+00 1.04e-01 6.68e+02 dihedral pdb=" C4' C U 74 " pdb=" C3' C U 74 " pdb=" C2' C U 74 " pdb=" C1' C U 74 " ideal model delta sinusoidal sigma weight residual 36.34 -34.32 70.66 1 3.10e+00 1.04e-01 6.68e+02 ... (remaining 18957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4117 0.057 - 0.113: 663 0.113 - 0.170: 50 0.170 - 0.226: 50 0.226 - 0.283: 40 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C2' C X 74 " pdb=" C3' C X 74 " pdb=" O2' C X 74 " pdb=" C1' C X 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' C I 74 " pdb=" C3' C I 74 " pdb=" O2' C I 74 " pdb=" C1' C I 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' C E 74 " pdb=" C3' C E 74 " pdb=" O2' C E 74 " pdb=" C1' C E 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4917 not shown) Planarity restraints: 5050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 73 " -0.025 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C F 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C F 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C F 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C F 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C F 73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C F 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C F 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " -0.025 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C U 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C U 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C U 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C U 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C I 73 " -0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C I 73 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C I 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C I 73 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C I 73 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C I 73 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C I 73 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C I 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C I 73 " 0.005 2.00e-02 2.50e+03 ... (remaining 5047 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.43: 120 1.43 - 2.30: 200 2.30 - 3.17: 26141 3.17 - 4.03: 81053 4.03 - 4.90: 150190 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257704 Sorted by model distance: nonbonded pdb=" CE1 TYR Y 23 " pdb=" CZ ARG 1 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR J 23 " pdb=" CZ ARG M 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR G 23 " pdb=" CZ ARG J 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR A 23 " pdb=" CZ ARG C 78 " model vdw 0.568 3.570 nonbonded pdb=" CE1 TYR P 23 " pdb=" CZ ARG S 78 " model vdw 0.568 3.570 ... (remaining 257699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain '1' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain '2' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain '0' selection = chain '3' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 30720 Z= 0.185 Angle : 0.617 5.983 41710 Z= 0.330 Chirality : 0.052 0.283 4920 Planarity : 0.003 0.028 5050 Dihedral : 15.541 82.962 12080 Min Nonbonded Distance : 0.568 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3640 helix: 1.16 (0.11), residues: 2270 sheet: -0.79 (0.30), residues: 210 loop : -0.63 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 78 TYR 0.018 0.002 TYR V 53 PHE 0.014 0.002 PHE C 169 TRP 0.006 0.002 TRP C 123 HIS 0.005 0.001 HIS G 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (30720) covalent geometry : angle 0.61673 / 0.33 (41710) hydrogen bonds : bond 0.13114 / 8.98 ( 1680) hydrogen bonds : angle 5.49334 / 3.75 ( 4920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.6685 (tp30) cc_final: 0.6247 (mm-30) REVERT: C 55 LYS cc_start: 0.7701 (mppt) cc_final: 0.7426 (mppt) REVERT: C 180 LEU cc_start: 0.8539 (mt) cc_final: 0.8254 (mt) REVERT: J 85 ASN cc_start: 0.8590 (m-40) cc_final: 0.8216 (m110) REVERT: J 249 MET cc_start: 0.8336 (mmt) cc_final: 0.8045 (mmp) REVERT: J 281 GLU cc_start: 0.6960 (tp30) cc_final: 0.6746 (tp30) REVERT: K 12 TYR cc_start: 0.7451 (m-80) cc_final: 0.7173 (m-10) REVERT: K 16 MET cc_start: 0.4604 (mmm) cc_final: 0.4281 (mmt) REVERT: M 200 ARG cc_start: 0.7529 (ptp90) cc_final: 0.7326 (ptt-90) REVERT: N 12 TYR cc_start: 0.7298 (m-80) cc_final: 0.7067 (m-10) REVERT: P 281 GLU cc_start: 0.6681 (tp30) cc_final: 0.6243 (mm-30) REVERT: S 55 LYS cc_start: 0.7698 (mppt) cc_final: 0.7427 (mppt) REVERT: S 180 LEU cc_start: 0.8541 (mt) cc_final: 0.8249 (mt) REVERT: Y 85 ASN cc_start: 0.8590 (m-40) cc_final: 0.8219 (m110) REVERT: Y 249 MET cc_start: 0.8335 (mmt) cc_final: 0.8044 (mmp) REVERT: Y 281 GLU cc_start: 0.6962 (tp30) cc_final: 0.6750 (tp30) REVERT: Z 12 TYR cc_start: 0.7452 (m-80) cc_final: 0.7174 (m-10) REVERT: Z 16 MET cc_start: 0.4605 (mmm) cc_final: 0.4276 (mmt) REVERT: 2 12 TYR cc_start: 0.7300 (m-80) cc_final: 0.7070 (m-10) outliers start: 0 outliers final: 2 residues processed: 437 average time/residue: 0.7071 time to fit residues: 357.9570 Evaluate side-chains 301 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain S residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 112 GLN A 306 GLN A 365 ASN C 42 GLN C 112 GLN C 306 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN G 42 GLN G 112 GLN G 306 GLN G 365 ASN J 112 GLN J 306 GLN J 365 ASN M 42 GLN M 85 ASN M 112 GLN M 279 GLN M 306 GLN M 365 ASN P 42 GLN P 112 GLN P 306 GLN P 365 ASN S 42 GLN S 112 GLN S 306 GLN S 365 ASN V 42 GLN V 112 GLN V 306 GLN V 365 ASN Y 112 GLN Y 306 GLN Y 365 ASN 1 42 GLN 1 85 ASN 1 112 GLN 1 279 GLN 1 306 GLN 1 365 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.184876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135070 restraints weight = 34942.051| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.74 r_work: 0.3287 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30720 Z= 0.155 Angle : 0.708 9.866 41710 Z= 0.325 Chirality : 0.056 0.588 4920 Planarity : 0.004 0.047 5050 Dihedral : 12.037 73.500 5116 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.89 % Allowed : 7.34 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.14), residues: 3640 helix: 1.61 (0.11), residues: 2310 sheet: -0.61 (0.32), residues: 210 loop : -0.37 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 208 TYR 0.029 0.002 TYR G 354 PHE 0.012 0.002 PHE P 169 TRP 0.003 0.001 TRP A 123 HIS 0.003 0.001 HIS G 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30720) covalent geometry : angle 0.70757 / 0.33 (41710) hydrogen bonds : bond 0.04608 / 3.12 ( 1680) hydrogen bonds : angle 4.43018 / 3.01 ( 4920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 322 time to evaluate : 0.955 Fit side-chains REVERT: A 281 GLU cc_start: 0.6435 (tp30) cc_final: 0.5852 (mm-30) REVERT: C 55 LYS cc_start: 0.7694 (mppt) cc_final: 0.7464 (mmmm) REVERT: C 135 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6444 (ttp) REVERT: C 180 LEU cc_start: 0.8549 (mt) cc_final: 0.8298 (mt) REVERT: C 200 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7517 (ptp90) REVERT: C 339 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8057 (mtp180) REVERT: G 40 LEU cc_start: 0.8196 (mp) cc_final: 0.7976 (mp) REVERT: G 281 GLU cc_start: 0.6319 (tp30) cc_final: 0.5670 (mm-30) REVERT: J 281 GLU cc_start: 0.6284 (tp30) cc_final: 0.5911 (mm-30) REVERT: K 12 TYR cc_start: 0.7038 (m-80) cc_final: 0.6697 (m-10) REVERT: M 200 ARG cc_start: 0.7780 (ptp90) cc_final: 0.7499 (ptt-90) REVERT: M 281 GLU cc_start: 0.6513 (tp30) cc_final: 0.5849 (mm-30) REVERT: N 12 TYR cc_start: 0.6934 (m-80) cc_final: 0.6708 (m-10) REVERT: P 281 GLU cc_start: 0.6438 (tp30) cc_final: 0.5863 (mm-30) REVERT: S 55 LYS cc_start: 0.7710 (mppt) cc_final: 0.7473 (mmmm) REVERT: S 135 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6451 (ttp) REVERT: S 180 LEU cc_start: 0.8541 (mt) cc_final: 0.8292 (mt) REVERT: S 200 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7530 (ptp90) REVERT: S 339 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8040 (mtp180) REVERT: V 40 LEU cc_start: 0.8202 (mp) cc_final: 0.7981 (mp) REVERT: V 281 GLU cc_start: 0.6314 (tp30) cc_final: 0.5660 (mm-30) REVERT: Y 281 GLU cc_start: 0.6288 (tp30) cc_final: 0.5910 (mm-30) REVERT: Z 12 TYR cc_start: 0.7039 (m-80) cc_final: 0.6700 (m-10) REVERT: 1 281 GLU cc_start: 0.6498 (tp30) cc_final: 0.5826 (mm-30) REVERT: 2 12 TYR cc_start: 0.6934 (m-80) cc_final: 0.6709 (m-10) outliers start: 28 outliers final: 16 residues processed: 330 average time/residue: 0.6046 time to fit residues: 232.3328 Evaluate side-chains 303 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 135 MET Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain 1 residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 82 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 339 optimal weight: 0.1980 chunk 271 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN G 344 ASN J 320 ASN M 320 ASN P 320 ASN V 344 ASN Y 320 ASN 1 320 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.181700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131044 restraints weight = 34935.198| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.83 r_work: 0.3253 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 30720 Z= 0.199 Angle : 0.665 8.566 41710 Z= 0.316 Chirality : 0.051 0.325 4920 Planarity : 0.004 0.054 5050 Dihedral : 12.626 112.790 5110 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.96 % Allowed : 7.97 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3640 helix: 1.57 (0.11), residues: 2300 sheet: -0.70 (0.33), residues: 210 loop : -0.40 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 341 TYR 0.036 0.002 TYR S 53 PHE 0.015 0.002 PHE A 169 TRP 0.005 0.001 TRP C 261 HIS 0.004 0.001 HIS V 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (30720) covalent geometry : angle 0.66520 / 0.32 (41710) hydrogen bonds : bond 0.04825 / 3.27 ( 1680) hydrogen bonds : angle 4.38247 / 2.97 ( 4920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 315 time to evaluate : 1.168 Fit side-chains REVERT: A 281 GLU cc_start: 0.6744 (tp30) cc_final: 0.6205 (mm-30) REVERT: C 76 SER cc_start: 0.7439 (t) cc_final: 0.7100 (m) REVERT: C 135 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6284 (ttp) REVERT: C 180 LEU cc_start: 0.8587 (mt) cc_final: 0.8312 (mt) REVERT: C 281 GLU cc_start: 0.6434 (tp30) cc_final: 0.5406 (mt-10) REVERT: G 148 GLN cc_start: 0.6844 (tm-30) cc_final: 0.6568 (tm-30) REVERT: G 272 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5659 (ttt) REVERT: G 281 GLU cc_start: 0.6407 (tp30) cc_final: 0.5798 (mm-30) REVERT: J 26 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7840 (mtmt) REVERT: J 281 GLU cc_start: 0.6256 (tp30) cc_final: 0.5803 (mm-30) REVERT: J 337 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7431 (ppp) REVERT: K 12 TYR cc_start: 0.7126 (m-80) cc_final: 0.6753 (m-10) REVERT: M 200 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7483 (ptt-90) REVERT: M 215 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: M 281 GLU cc_start: 0.6404 (tp30) cc_final: 0.6156 (mm-30) REVERT: N 12 TYR cc_start: 0.7046 (m-80) cc_final: 0.6780 (m-10) REVERT: P 281 GLU cc_start: 0.6732 (tp30) cc_final: 0.6191 (mm-30) REVERT: S 76 SER cc_start: 0.7425 (t) cc_final: 0.7088 (m) REVERT: S 135 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6298 (ttp) REVERT: S 180 LEU cc_start: 0.8580 (mt) cc_final: 0.8303 (mt) REVERT: S 281 GLU cc_start: 0.6442 (tp30) cc_final: 0.5419 (mt-10) REVERT: V 148 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6597 (tm-30) REVERT: V 272 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5674 (ttt) REVERT: V 281 GLU cc_start: 0.6395 (tp30) cc_final: 0.5785 (mm-30) REVERT: Y 26 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7826 (mtmt) REVERT: Y 281 GLU cc_start: 0.6233 (tp30) cc_final: 0.5770 (mm-30) REVERT: Y 337 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7411 (ppp) REVERT: Z 12 TYR cc_start: 0.7116 (m-80) cc_final: 0.6747 (m-10) REVERT: 1 215 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: 1 281 GLU cc_start: 0.6411 (tp30) cc_final: 0.6159 (mm-30) REVERT: 2 12 TYR cc_start: 0.7047 (m-80) cc_final: 0.6778 (m-10) outliers start: 62 outliers final: 40 residues processed: 343 average time/residue: 0.6588 time to fit residues: 265.5222 Evaluate side-chains 340 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 272 MET Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 135 MET Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 272 MET Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 337 MET Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 215 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 295 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 296 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN P 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.183179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133139 restraints weight = 34721.618| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.73 r_work: 0.3261 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30720 Z= 0.144 Angle : 0.618 8.253 41710 Z= 0.291 Chirality : 0.048 0.289 4920 Planarity : 0.004 0.056 5050 Dihedral : 12.749 122.621 5110 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.84 % Allowed : 9.94 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3640 helix: 1.78 (0.11), residues: 2300 sheet: -0.95 (0.32), residues: 210 loop : -0.38 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 341 TYR 0.035 0.002 TYR A 53 PHE 0.012 0.002 PHE P 224 TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS G 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (30720) covalent geometry : angle 0.61784 / 0.29 (41710) hydrogen bonds : bond 0.04223 / 2.86 ( 1680) hydrogen bonds : angle 4.20333 / 2.85 ( 4920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 0.848 Fit side-chains REVERT: A 22 GLN cc_start: 0.8182 (mp10) cc_final: 0.7595 (tp40) REVERT: C 76 SER cc_start: 0.7353 (t) cc_final: 0.7044 (m) REVERT: C 94 LEU cc_start: 0.7905 (tp) cc_final: 0.7441 (mp) REVERT: G 148 GLN cc_start: 0.6819 (tm-30) cc_final: 0.6536 (tm-30) REVERT: G 281 GLU cc_start: 0.6198 (tp30) cc_final: 0.5719 (mm-30) REVERT: K 12 TYR cc_start: 0.7143 (m-80) cc_final: 0.6760 (m-10) REVERT: M 200 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7434 (ptt-90) REVERT: N 12 TYR cc_start: 0.7058 (m-80) cc_final: 0.6802 (m-10) REVERT: N 16 MET cc_start: 0.4665 (mmm) cc_final: 0.4061 (mmp) REVERT: P 22 GLN cc_start: 0.8154 (mp10) cc_final: 0.7592 (tp40) REVERT: P 113 MET cc_start: 0.5376 (mmp) cc_final: 0.5175 (mmp) REVERT: S 76 SER cc_start: 0.7343 (t) cc_final: 0.7034 (m) REVERT: S 94 LEU cc_start: 0.7910 (tp) cc_final: 0.7441 (mp) REVERT: V 148 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6538 (tm-30) REVERT: V 281 GLU cc_start: 0.6173 (tp30) cc_final: 0.5699 (mm-30) REVERT: Z 12 TYR cc_start: 0.7135 (m-80) cc_final: 0.6754 (m-10) REVERT: 2 12 TYR cc_start: 0.7045 (m-80) cc_final: 0.6790 (m-10) outliers start: 58 outliers final: 38 residues processed: 331 average time/residue: 0.5845 time to fit residues: 227.6706 Evaluate side-chains 321 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 79 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.179994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125517 restraints weight = 34749.594| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.86 r_work: 0.3204 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30720 Z= 0.227 Angle : 0.690 9.027 41710 Z= 0.327 Chirality : 0.051 0.297 4920 Planarity : 0.004 0.058 5050 Dihedral : 12.761 134.178 5110 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.66 % Allowed : 9.87 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.14), residues: 3640 helix: 1.57 (0.11), residues: 2300 sheet: -1.11 (0.32), residues: 210 loop : -0.52 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 341 TYR 0.035 0.002 TYR 1 53 PHE 0.017 0.002 PHE P 169 TRP 0.006 0.001 TRP C 261 HIS 0.004 0.001 HIS V 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (30720) covalent geometry : angle 0.68975 / 0.33 (41710) hydrogen bonds : bond 0.04859 / 3.29 ( 1680) hydrogen bonds : angle 4.37073 / 2.97 ( 4920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 1.301 Fit side-chains REVERT: A 22 GLN cc_start: 0.8153 (mp10) cc_final: 0.7693 (tp40) REVERT: C 94 LEU cc_start: 0.8005 (tp) cc_final: 0.7707 (mp) REVERT: C 180 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8309 (mt) REVERT: G 148 GLN cc_start: 0.6976 (tm-30) cc_final: 0.6668 (tm-30) REVERT: J 26 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7898 (mtmt) REVERT: J 215 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: M 22 GLN cc_start: 0.8093 (mp10) cc_final: 0.7595 (tp40) REVERT: M 200 ARG cc_start: 0.7846 (ptp90) cc_final: 0.7479 (ptt-90) REVERT: M 215 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: N 12 TYR cc_start: 0.7133 (m-80) cc_final: 0.6929 (m-10) REVERT: P 22 GLN cc_start: 0.8133 (mp10) cc_final: 0.7686 (tp40) REVERT: S 94 LEU cc_start: 0.8005 (tp) cc_final: 0.7707 (mp) REVERT: V 148 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6664 (tm-30) REVERT: Y 26 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7897 (mtmt) REVERT: Y 215 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: Z 12 TYR cc_start: 0.7108 (m-80) cc_final: 0.6807 (m-10) REVERT: 1 22 GLN cc_start: 0.8096 (mp10) cc_final: 0.7589 (tp40) REVERT: 1 215 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: 2 12 TYR cc_start: 0.7162 (m-80) cc_final: 0.6935 (m-10) outliers start: 84 outliers final: 63 residues processed: 336 average time/residue: 0.6234 time to fit residues: 248.8940 Evaluate side-chains 346 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 276 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 215 GLU Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 186 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 297 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 226 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.180959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132590 restraints weight = 34633.572| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.58 r_work: 0.3271 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30720 Z= 0.182 Angle : 0.669 10.343 41710 Z= 0.313 Chirality : 0.050 0.290 4920 Planarity : 0.004 0.056 5050 Dihedral : 12.743 134.040 5110 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.47 % Allowed : 11.39 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.14), residues: 3640 helix: 1.62 (0.11), residues: 2320 sheet: -1.14 (0.32), residues: 210 loop : -0.44 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 341 TYR 0.031 0.002 TYR V 53 PHE 0.014 0.002 PHE P 169 TRP 0.004 0.001 TRP G 261 HIS 0.004 0.001 HIS G 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (30720) covalent geometry : angle 0.66927 / 0.31 (41710) hydrogen bonds : bond 0.04449 / 3.02 ( 1680) hydrogen bonds : angle 4.27088 / 2.90 ( 4920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 283 time to evaluate : 1.013 Fit side-chains REVERT: A 22 GLN cc_start: 0.8114 (mp10) cc_final: 0.7760 (tp-100) REVERT: C 94 LEU cc_start: 0.8077 (tp) cc_final: 0.7874 (mp) REVERT: C 180 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8327 (mt) REVERT: G 148 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6828 (tm-30) REVERT: J 26 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7854 (mtmt) REVERT: J 94 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7373 (mp) REVERT: M 22 GLN cc_start: 0.8066 (mp10) cc_final: 0.7679 (tp40) REVERT: M 215 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: N 16 MET cc_start: 0.4667 (mmm) cc_final: 0.3904 (mmp) REVERT: P 22 GLN cc_start: 0.8083 (mp10) cc_final: 0.7756 (tp-100) REVERT: S 94 LEU cc_start: 0.8080 (tp) cc_final: 0.7873 (mp) REVERT: V 148 GLN cc_start: 0.7040 (tm-30) cc_final: 0.6807 (tm-30) REVERT: Y 26 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7858 (mtmt) REVERT: Y 94 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7377 (mp) REVERT: 1 22 GLN cc_start: 0.8069 (mp10) cc_final: 0.7684 (tp40) REVERT: 1 215 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: 2 16 MET cc_start: 0.4667 (mmm) cc_final: 0.3974 (mmp) outliers start: 78 outliers final: 62 residues processed: 323 average time/residue: 0.6317 time to fit residues: 242.4807 Evaluate side-chains 342 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 135 MET Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 256 optimal weight: 0.6980 chunk 354 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 342 optimal weight: 0.7980 chunk 268 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 239 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.182587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134347 restraints weight = 34420.163| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.73 r_work: 0.3278 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30720 Z= 0.138 Angle : 0.640 10.166 41710 Z= 0.297 Chirality : 0.048 0.295 4920 Planarity : 0.004 0.056 5050 Dihedral : 12.726 132.679 5110 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.15 % Allowed : 11.99 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 3640 helix: 1.86 (0.11), residues: 2320 sheet: -1.06 (0.32), residues: 210 loop : -0.39 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 341 TYR 0.036 0.002 TYR Z 12 PHE 0.012 0.001 PHE P 224 TRP 0.003 0.001 TRP A 123 HIS 0.002 0.001 HIS V 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (30720) covalent geometry : angle 0.64008 / 0.30 (41710) hydrogen bonds : bond 0.04044 / 2.74 ( 1680) hydrogen bonds : angle 4.12429 / 2.80 ( 4920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 284 time to evaluate : 1.279 Fit side-chains REVERT: A 22 GLN cc_start: 0.8112 (mp10) cc_final: 0.7745 (tp40) REVERT: C 180 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8289 (mt) REVERT: C 339 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8091 (mtp180) REVERT: D 16 MET cc_start: 0.4885 (mmm) cc_final: 0.4576 (tpt) REVERT: G 148 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6839 (tm-30) REVERT: J 94 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7392 (mp) REVERT: J 113 MET cc_start: 0.5976 (mmp) cc_final: 0.5757 (mmp) REVERT: K 12 TYR cc_start: 0.6777 (m-80) cc_final: 0.6472 (m-10) REVERT: M 22 GLN cc_start: 0.8059 (mp10) cc_final: 0.7698 (tp40) REVERT: P 22 GLN cc_start: 0.8065 (mp10) cc_final: 0.7743 (tp40) REVERT: S 339 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8091 (mtp180) REVERT: T 16 MET cc_start: 0.4873 (mmm) cc_final: 0.4562 (tpt) REVERT: V 148 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6833 (tm-30) REVERT: Y 94 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7399 (mp) REVERT: 1 22 GLN cc_start: 0.8062 (mp10) cc_final: 0.7696 (tp40) outliers start: 68 outliers final: 55 residues processed: 328 average time/residue: 0.6672 time to fit residues: 259.3371 Evaluate side-chains 326 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 135 MET Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 321 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 336 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN G 150 GLN J 270 ASN M 150 GLN P 270 ASN V 150 GLN Y 270 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.180907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132596 restraints weight = 34533.188| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.63 r_work: 0.3254 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30720 Z= 0.191 Angle : 0.691 11.490 41710 Z= 0.322 Chirality : 0.050 0.286 4920 Planarity : 0.004 0.055 5050 Dihedral : 12.713 133.652 5110 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.47 % Allowed : 12.44 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3640 helix: 1.75 (0.11), residues: 2320 sheet: -1.05 (0.33), residues: 210 loop : -0.46 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 341 TYR 0.031 0.002 TYR C 53 PHE 0.015 0.002 PHE A 169 TRP 0.005 0.001 TRP S 261 HIS 0.003 0.001 HIS V 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (30720) covalent geometry : angle 0.69074 / 0.32 (41710) hydrogen bonds : bond 0.04479 / 3.04 ( 1680) hydrogen bonds : angle 4.24700 / 2.88 ( 4920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 294 time to evaluate : 1.091 Fit side-chains REVERT: A 22 GLN cc_start: 0.8123 (mp10) cc_final: 0.7765 (tp-100) REVERT: A 26 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7905 (mtmt) REVERT: C 180 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8331 (mt) REVERT: G 22 GLN cc_start: 0.8094 (mp10) cc_final: 0.7621 (mm110) REVERT: G 148 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6835 (tm-30) REVERT: H 16 MET cc_start: 0.4653 (mmm) cc_final: 0.4151 (mmp) REVERT: J 26 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7883 (mtmt) REVERT: J 94 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7501 (mp) REVERT: J 270 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7122 (t0) REVERT: K 12 TYR cc_start: 0.6732 (m-80) cc_final: 0.6392 (m-10) REVERT: M 22 GLN cc_start: 0.8108 (mp10) cc_final: 0.7780 (tp40) REVERT: M 94 LEU cc_start: 0.8049 (tp) cc_final: 0.7712 (mp) REVERT: M 215 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: N 12 TYR cc_start: 0.6730 (m-80) cc_final: 0.6483 (m-10) REVERT: N 16 MET cc_start: 0.4844 (mmm) cc_final: 0.4099 (mmp) REVERT: P 22 GLN cc_start: 0.8087 (mp10) cc_final: 0.7769 (tp-100) REVERT: P 26 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7906 (mtmt) REVERT: V 22 GLN cc_start: 0.8101 (mp10) cc_final: 0.7629 (mm110) REVERT: V 148 GLN cc_start: 0.7057 (tm-30) cc_final: 0.6821 (tm-30) REVERT: W 16 MET cc_start: 0.4668 (mmm) cc_final: 0.4171 (mmp) REVERT: Y 26 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7873 (mtmt) REVERT: Y 94 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7501 (mp) REVERT: Y 270 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7105 (t0) REVERT: Z 12 TYR cc_start: 0.6814 (m-80) cc_final: 0.6446 (m-10) REVERT: 1 22 GLN cc_start: 0.8111 (mp10) cc_final: 0.7777 (tp40) REVERT: 1 94 LEU cc_start: 0.8049 (tp) cc_final: 0.7722 (mp) REVERT: 1 215 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: 2 12 TYR cc_start: 0.6707 (m-80) cc_final: 0.6456 (m-10) REVERT: 2 16 MET cc_start: 0.4821 (mmm) cc_final: 0.4508 (tpt) outliers start: 78 outliers final: 63 residues processed: 343 average time/residue: 0.6488 time to fit residues: 262.8403 Evaluate side-chains 346 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 272 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 306 GLN Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 10 ASP Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 26 LYS Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 306 GLN Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 10 ASP Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 94 LEU Chi-restraints excluded: chain Y residue 135 MET Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 270 ASN Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 10 ASP Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 224 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 354 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 281 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 ASN S 270 ASN 1 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.183051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134739 restraints weight = 34602.946| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.67 r_work: 0.3307 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30720 Z= 0.131 Angle : 0.662 12.536 41710 Z= 0.306 Chirality : 0.048 0.300 4920 Planarity : 0.004 0.054 5050 Dihedral : 12.735 132.803 5110 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.99 % Allowed : 13.39 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3640 helix: 1.97 (0.11), residues: 2330 sheet: -0.92 (0.33), residues: 210 loop : -0.31 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 341 TYR 0.030 0.001 TYR C 53 PHE 0.010 0.001 PHE A 224 TRP 0.004 0.001 TRP J 123 HIS 0.002 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (30720) covalent geometry : angle 0.66209 / 0.31 (41710) hydrogen bonds : bond 0.03966 / 2.69 ( 1680) hydrogen bonds : angle 4.14002 / 2.81 ( 4920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.304 Fit side-chains REVERT: A 22 GLN cc_start: 0.8091 (mp10) cc_final: 0.7760 (tp40) REVERT: C 180 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8300 (mt) REVERT: C 339 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7905 (mtp180) REVERT: G 22 GLN cc_start: 0.8078 (mp10) cc_final: 0.7617 (mm110) REVERT: G 148 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6819 (tm-30) REVERT: G 341 ARG cc_start: 0.7453 (ptm-80) cc_final: 0.6420 (mtm110) REVERT: H 16 MET cc_start: 0.4417 (mmm) cc_final: 0.3964 (mmp) REVERT: K 12 TYR cc_start: 0.6709 (m-80) cc_final: 0.6410 (m-10) REVERT: M 22 GLN cc_start: 0.8077 (mp10) cc_final: 0.7787 (tp40) REVERT: M 94 LEU cc_start: 0.8021 (tp) cc_final: 0.7725 (mp) REVERT: N 12 TYR cc_start: 0.6731 (m-80) cc_final: 0.6484 (m-10) REVERT: N 16 MET cc_start: 0.4801 (mmm) cc_final: 0.4184 (mmp) REVERT: P 22 GLN cc_start: 0.8068 (mp10) cc_final: 0.7764 (tp40) REVERT: S 339 ARG cc_start: 0.8380 (mtp85) cc_final: 0.7995 (mtp180) REVERT: V 22 GLN cc_start: 0.8094 (mp10) cc_final: 0.7631 (mm110) REVERT: V 148 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6794 (tm-30) REVERT: V 341 ARG cc_start: 0.7463 (ptm-80) cc_final: 0.6457 (mtm110) REVERT: W 16 MET cc_start: 0.4430 (mmm) cc_final: 0.3980 (mmp) REVERT: Z 12 TYR cc_start: 0.6775 (m-80) cc_final: 0.6428 (m-10) REVERT: 1 22 GLN cc_start: 0.8093 (mp10) cc_final: 0.7784 (tp40) REVERT: 1 94 LEU cc_start: 0.8021 (tp) cc_final: 0.7730 (mp) REVERT: 2 12 TYR cc_start: 0.6722 (m-80) cc_final: 0.6478 (m-10) REVERT: 2 16 MET cc_start: 0.4767 (mmm) cc_final: 0.4145 (mmp) outliers start: 63 outliers final: 45 residues processed: 318 average time/residue: 0.6112 time to fit residues: 230.7670 Evaluate side-chains 320 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 337 MET Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 135 MET Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 103 optimal weight: 0.0870 chunk 147 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 ASN J 270 ASN M 270 ASN Y 270 ASN 1 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133456 restraints weight = 34467.564| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.72 r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30720 Z= 0.156 Angle : 0.690 13.205 41710 Z= 0.320 Chirality : 0.048 0.289 4920 Planarity : 0.004 0.053 5050 Dihedral : 12.695 133.315 5110 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.96 % Allowed : 13.70 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3640 helix: 1.95 (0.11), residues: 2330 sheet: -0.91 (0.32), residues: 210 loop : -0.27 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 341 TYR 0.026 0.002 TYR J 53 PHE 0.013 0.002 PHE A 169 TRP 0.004 0.001 TRP Y 123 HIS 0.003 0.001 HIS Y 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (30720) covalent geometry : angle 0.68995 / 0.32 (41710) hydrogen bonds : bond 0.04182 / 2.84 ( 1680) hydrogen bonds : angle 4.19153 / 2.84 ( 4920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 1.105 Fit side-chains REVERT: A 22 GLN cc_start: 0.8101 (mp10) cc_final: 0.7745 (tp-100) REVERT: A 341 ARG cc_start: 0.7646 (ptm-80) cc_final: 0.6250 (mtp-110) REVERT: B 16 MET cc_start: 0.4043 (mmm) cc_final: 0.3715 (mmp) REVERT: C 180 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8275 (mt) REVERT: C 339 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7966 (mtp180) REVERT: C 341 ARG cc_start: 0.7720 (ptm-80) cc_final: 0.6570 (mtm110) REVERT: G 22 GLN cc_start: 0.8079 (mp10) cc_final: 0.7581 (mm110) REVERT: G 148 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6842 (tm-30) REVERT: G 341 ARG cc_start: 0.7446 (ptm-80) cc_final: 0.6388 (mtm110) REVERT: H 16 MET cc_start: 0.4394 (mmm) cc_final: 0.3963 (mmp) REVERT: J 26 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7870 (mtmt) REVERT: K 12 TYR cc_start: 0.6614 (m-80) cc_final: 0.6368 (m-10) REVERT: K 16 MET cc_start: 0.4378 (mmm) cc_final: 0.3686 (mmp) REVERT: M 22 GLN cc_start: 0.8118 (mp10) cc_final: 0.7733 (tp40) REVERT: M 94 LEU cc_start: 0.8049 (tp) cc_final: 0.7759 (mp) REVERT: M 200 ARG cc_start: 0.7853 (ptp90) cc_final: 0.7611 (ptt-90) REVERT: P 22 GLN cc_start: 0.8074 (mp10) cc_final: 0.7750 (tp-100) REVERT: P 341 ARG cc_start: 0.7648 (ptm-80) cc_final: 0.6249 (mtp-110) REVERT: Q 16 MET cc_start: 0.4058 (mmm) cc_final: 0.3725 (mmp) REVERT: S 339 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7998 (mtp180) REVERT: S 341 ARG cc_start: 0.7706 (ptm-80) cc_final: 0.6569 (mtm110) REVERT: V 22 GLN cc_start: 0.8085 (mp10) cc_final: 0.7591 (mm110) REVERT: V 148 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6817 (tm-30) REVERT: V 341 ARG cc_start: 0.7442 (ptm-80) cc_final: 0.6383 (mtm110) REVERT: W 16 MET cc_start: 0.4409 (mmm) cc_final: 0.3987 (mmp) REVERT: Y 26 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7863 (mtmt) REVERT: Z 12 TYR cc_start: 0.6660 (m-80) cc_final: 0.6375 (m-10) REVERT: Z 16 MET cc_start: 0.4380 (mmm) cc_final: 0.3686 (mmp) REVERT: 1 22 GLN cc_start: 0.8112 (mp10) cc_final: 0.7759 (tp40) REVERT: 1 94 LEU cc_start: 0.8048 (tp) cc_final: 0.7764 (mp) outliers start: 62 outliers final: 45 residues processed: 321 average time/residue: 0.6340 time to fit residues: 241.9650 Evaluate side-chains 320 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 175 THR Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 124 VAL Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain Y residue 26 LYS Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 175 THR Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 175 THR Chi-restraints excluded: chain 1 residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 254 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 343 optimal weight: 0.6980 chunk 314 optimal weight: 1.9990 chunk 123 optimal weight: 0.0870 chunk 221 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 349 optimal weight: 0.8980 chunk 258 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 GLN G 270 ASN J 328 ASN J 365 ASN M 328 ASN Y 328 ASN 1 328 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.183039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133397 restraints weight = 34821.993| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.77 r_work: 0.3284 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30720 Z= 0.138 Angle : 0.672 13.061 41710 Z= 0.310 Chirality : 0.047 0.299 4920 Planarity : 0.004 0.052 5050 Dihedral : 12.703 132.805 5110 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.68 % Allowed : 13.83 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3640 helix: 2.06 (0.11), residues: 2330 sheet: -0.84 (0.32), residues: 210 loop : -0.17 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 341 TYR 0.026 0.001 TYR J 53 PHE 0.011 0.001 PHE M 169 TRP 0.004 0.001 TRP Y 123 HIS 0.003 0.001 HIS J 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (30720) covalent geometry : angle 0.67228 / 0.31 (41710) hydrogen bonds : bond 0.04000 / 2.71 ( 1680) hydrogen bonds : angle 4.13240 / 2.80 ( 4920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10497.27 seconds wall clock time: 179 minutes 50.17 seconds (10790.17 seconds total)